Code formatting

anno-gui/src/main/java/org/genesys2/anno/converter/RowConverter.java

@@ -13,7 +13,6 @@ import org.apache.commons.lang3.ArrayUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.log4j.Logger;
 import org.genesys2.anno.gui.ColumnDefs;
-import org.genesys2.anno.gui.DataSourceSheet;
 import org.genesys2.anno.gui.IDataSourceSheet;
 import org.genesys2.anno.model.Column;
 import org.genesys2.anno.model.ColumnDef;

anno-gui/src/main/java/org/genesys2/anno/gui/AppWindow.java

@@ -19,7 +19,6 @@ package org.genesys2.anno.gui;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
 import java.util.concurrent.ExecutorService;
@@ -119,7 +118,7 @@ public class AppWindow {
 
 		@Override
 		public String getText(Object element) {
-//			_log.debug("getText " + element);
+			// _log.debug("getText " + element);
 			if (element instanceof DataSourceFile) {
 				return ((DataSourceFile) element).getFile().getName();
 			}
@@ -164,15 +163,15 @@ public class AppWindow {
 			if (parentElement instanceof DataSourceFile) {
 				return ((DataSourceFile) parentElement).getSheets().toArray();
 			}
-            if (parentElement instanceof JdbcDataSource) {
-                return ((JdbcDataSource) parentElement).getSheets().toArray();
-            }
+			if (parentElement instanceof JdbcDataSource) {
+				return ((JdbcDataSource) parentElement).getSheets().toArray();
+			}
 			if (parentElement instanceof DataSourceSheet) {
 				return null;
 			}
-            if (parentElement instanceof JdbcDataSourceSheet) {
-                return null;
-            }
+			if (parentElement instanceof JdbcDataSourceSheet) {
+				return null;
+			}
 			return new Object[] { "Item 0", "Item 1", "Item 2" };
 		}
 
@@ -183,7 +182,7 @@ public class AppWindow {
 
 		@Override
 		public boolean hasChildren(Object element) {
-//			_log.debug("hasChildren " + element + " " + element.getClass());
+			// _log.debug("hasChildren " + element + " " + element.getClass());
 
 			if (element instanceof DwcaBuilder) {
 				return ((DwcaBuilder) element).getFileRoots().size() > 0;
@@ -191,15 +190,15 @@ public class AppWindow {
 			if (element instanceof DataSourceFile) {
 				return ((DataSourceFile) element).getSheets().size() > 0;
 			}
-            if (element instanceof JdbcDataSource) {
-                return ((JdbcDataSource) element).getSheets().size() > 0;
-            }
+			if (element instanceof JdbcDataSource) {
+				return ((JdbcDataSource) element).getSheets().size() > 0;
+			}
 			if (element instanceof DataSourceSheet) {
 				return false;
 			}
-            if (element instanceof JdbcDataSourceSheet) {
-                return false;
-            }
+			if (element instanceof JdbcDataSourceSheet) {
+				return false;
+			}
 
 			return getChildren(element).length > 0;
 		}
@@ -382,32 +381,32 @@ public class AppWindow {
 		treeViewer.setContentProvider(new TreeContentProvider());
 		treeViewer.setInput(builder);
 
-        final MenuItem mntmAddFile = new MenuItem(filesTreeMenu, SWT.NONE);
-        mntmAddFile.addSelectionListener(new SelectionAdapter() {
-            @Override
-            public void widgetSelected(SelectionEvent arg0) {
-                Object selectedObject = ((IStructuredSelection) treeViewer.getSelection()).getFirstElement();
-                if (selectedObject instanceof JdbcDataSource) {
-                    addJdbcQuery((JdbcDataSource) selectedObject);
-                }
-                if (selectedObject instanceof DataSourceFile) {
-                    addSourceFile();
-                }
-            }
-        });
-
-        filesTreeMenu.addMenuListener(new MenuAdapter() {
-            @Override
-            public void menuShown(MenuEvent e) {
-                Object selectedObject = ((IStructuredSelection) treeViewer.getSelection()).getFirstElement();
-                if (selectedObject instanceof DataSourceFile) {
-                    mntmAddFile.setText("Add file");
-                }
-                if (selectedObject instanceof JdbcDataSource) {
-                    mntmAddFile.setText("Add SQL Query");
-                }
-            }
-        });
+		final MenuItem mntmAddFile = new MenuItem(filesTreeMenu, SWT.NONE);
+		mntmAddFile.addSelectionListener(new SelectionAdapter() {
+			@Override
+			public void widgetSelected(SelectionEvent arg0) {
+				Object selectedObject = ((IStructuredSelection) treeViewer.getSelection()).getFirstElement();
+				if (selectedObject instanceof JdbcDataSource) {
+					addJdbcQuery((JdbcDataSource) selectedObject);
+				}
+				if (selectedObject instanceof DataSourceFile) {
+					addSourceFile();
+				}
+			}
+		});
+
+		filesTreeMenu.addMenuListener(new MenuAdapter() {
+			@Override
+			public void menuShown(MenuEvent e) {
+				Object selectedObject = ((IStructuredSelection) treeViewer.getSelection()).getFirstElement();
+				if (selectedObject instanceof DataSourceFile) {
+					mntmAddFile.setText("Add file");
+				}
+				if (selectedObject instanceof JdbcDataSource) {
+					mntmAddFile.setText("Add SQL Query");
+				}
+			}
+		});
 
 		final MenuItem mntmRemoveFile = new MenuItem(filesTreeMenu, SWT.NONE);
 		mntmRemoveFile.addSelectionListener(new SelectionAdapter() {
@@ -518,31 +517,31 @@ public class AppWindow {
 					CTabItem newSheetTab = createTab(tabFolder, currentSheet);
 
 					// Load stuff
-                    if (selectedNode instanceof DataSourceSheet) {
-
-                        threadPool.execute(new Runnable() {
-
-                            @Override
-                            public void run() {
-                                try {
-                                    final List<Object[]> rows = dataSourceLoader.loadRows(currentSheet, 200);
-                                    currentSheet.updateData(rows);
-
-                                } catch (UnsupportedDataFormatException e) {
-                                    e.printStackTrace();
-                                } catch (FileNotFoundException e) {
-                                    e.printStackTrace();
-                                } catch (IOException e) {
-                                    e.printStackTrace();
-                                }
-                            }
-                        });
-                    }
-                    tabFolder.setSelection(newSheetTab);
-                }
-            }
-        });
-        sashForm_1.setWeights(new int[] { 4 });
+					if (selectedNode instanceof DataSourceSheet) {
+
+						threadPool.execute(new Runnable() {
+
+							@Override
+							public void run() {
+								try {
+									final List<Object[]> rows = dataSourceLoader.loadRows(currentSheet, 200);
+									currentSheet.updateData(rows);
+
+								} catch (UnsupportedDataFormatException e) {
+									e.printStackTrace();
+								} catch (FileNotFoundException e) {
+									e.printStackTrace();
+								} catch (IOException e) {
+									e.printStackTrace();
+								}
+							}
+						});
+					}
+					tabFolder.setSelection(newSheetTab);
+				}
+			}
+		});
+		sashForm_1.setWeights(new int[] { 4 });
 
 		ToolBar toolBar = new ToolBar(shlGenesysMagic, SWT.FLAT);
 		toolBar.setBackground(SWTResourceManager.getColor(SWT.COLOR_WIDGET_BACKGROUND));
@@ -608,15 +607,15 @@ public class AppWindow {
 		tltmPush.setText("Push");
 		tltmPush.setImage(pushDataIcon);
 
-        ToolItem tltmDatabase = new ToolItem(toolBar, SWT.NONE);
-        tltmDatabase.addSelectionListener(new SelectionAdapter() {
-            @Override
-            public void widgetSelected(SelectionEvent e) {
-              doDatabase();
-            }
-        });
-        tltmDatabase.setText("Add database");
-        m_bindingContext = initDataBindings();
+		ToolItem tltmDatabase = new ToolItem(toolBar, SWT.NONE);
+		tltmDatabase.addSelectionListener(new SelectionAdapter() {
+			@Override
+			public void widgetSelected(SelectionEvent e) {
+				doDatabase();
+			}
+		});
+		tltmDatabase.setText("Add database");
+		m_bindingContext = initDataBindings();
 	}
 
 	protected CTabItem createTab(CTabFolder tabFolder, IDataSourceSheet currentSheet) {
@@ -626,7 +625,7 @@ public class AppWindow {
 		tbtmOther.setText(currentSheet.getSheetName());
 		tbtmOther.setImage(spreadsheetIcon16);
 
-		final SheetDisplay sheetDisplay = (SheetDisplay) applicationContext.getBean("sheetDisplay", currentSheet, tabFolder,treeViewer, SWT.NONE);
+		final SheetDisplay sheetDisplay = (SheetDisplay) applicationContext.getBean("sheetDisplay", currentSheet, tabFolder, treeViewer, SWT.NONE);
 		tbtmOther.setControl(sheetDisplay);
 
 		tbtmOther.addDisposeListener(new DisposeListener() {
@@ -699,10 +698,10 @@ public class AppWindow {
 		settingsDialog.open();
 	}
 
-    protected void doDatabase() {
-        DatabaseDialog databaseDialog = (DatabaseDialog) applicationContext.getBean("databaseDialog",shlGenesysMagic,treeViewer, SWT.NONE);
-        databaseDialog.open();
-    }
+	protected void doDatabase() {
+		DatabaseDialog databaseDialog = (DatabaseDialog) applicationContext.getBean("databaseDialog", shlGenesysMagic, treeViewer, SWT.NONE);
+		databaseDialog.open();
+	}
 
 	protected void doAutomap() {
 		final IDataSourceSheet dss = getCurrentDataSourceSheet();
@@ -730,12 +729,12 @@ public class AppWindow {
 		return dss;
 	}
 
-    public void addJdbcQuery(JdbcDataSource dataSource) {
-        JdbcDataSourceSheet dataSourceSheet= new JdbcDataSourceSheet();
-        dataSourceSheet.setDatabaseSettings(dataSource.getSettings());
-        dataSource.addSheet(dataSourceSheet);
-        treeViewer.refresh();
-    }
+	public void addJdbcQuery(JdbcDataSource dataSource) {
+		JdbcDataSourceSheet dataSourceSheet = new JdbcDataSourceSheet();
+		dataSourceSheet.setDatabaseSettings(dataSource.getSettings());
+		dataSource.addSheet(dataSourceSheet);
+		treeViewer.refresh();
+	}
 
 	public void addSourceFile() {
 		FileDialog fd = new FileDialog(shlGenesysMagic, SWT.MULTI);

anno-gui/src/main/java/org/genesys2/anno/gui/AppWindow2.java

@@ -41,6 +41,7 @@ public class AppWindow2 {
 
 	/**
 	 * Launch the application.
+	 * 
 	 * @param args
 	 */
 	public static void main(String[] args) {
@@ -68,11 +69,11 @@ public class AppWindow2 {
 	}
 
 	public static boolean isMac() {
-	        if ( System.getProperty( "os.name" ).equals( "Mac OS X" ) ) {
-	            return true;
-	        }
-	        return false;
-	    }
+		if (System.getProperty("os.name").equals("Mac OS X")) {
+			return true;
+		}
+		return false;
+	}
 
 	/**
 	 * Create contents of the window.
@@ -83,21 +84,21 @@ public class AppWindow2 {
 		shlGenesysMagic.setSize(554, 374);
 		shlGenesysMagic.setText("Genesys Magic");
 		shlGenesysMagic.setLayout(new BorderLayout(5, 5));
-		
+
 		Menu menu = new Menu(shlGenesysMagic, SWT.BAR);
 		shlGenesysMagic.setMenuBar(menu);
-		
+
 		MenuItem mntmFile = new MenuItem(menu, SWT.CASCADE);
 		mntmFile.setText("File");
-		
+
 		Menu menu_1 = new Menu(mntmFile);
 		mntmFile.setMenu(menu_1);
-		
+
 		MenuItem mntmOpen = new MenuItem(menu_1, SWT.NONE);
 		mntmOpen.setText("Open");
-		
+
 		new MenuItem(menu_1, SWT.SEPARATOR);
-		
+
 		mntmQuit = new MenuItem(menu_1, SWT.NONE);
 		mntmQuit.addSelectionListener(new SelectionAdapter() {
 			@Override
@@ -107,60 +108,60 @@ public class AppWindow2 {
 			}
 		});
 		mntmQuit.setText("Quit");
-		
+
 		MenuItem mntmHelp = new MenuItem(menu, SWT.CASCADE);
 		mntmHelp.setText("Help");
-		
+
 		Menu menu_2 = new Menu(mntmHelp);
 		mntmHelp.setMenu(menu_2);
-		
+
 		MenuItem mntmAbout = new MenuItem(menu_2, SWT.NONE);
 		mntmAbout.setText("About");
-		
+
 		new MenuItem(menu_2, SWT.SEPARATOR);
-		
+
 		MenuItem mntmVersion = new MenuItem(menu_2, SWT.NONE);
 		mntmVersion.setText("Version...");
-		
+
 		SashForm sashForm = new SashForm(shlGenesysMagic, SWT.NONE);
 		sashForm.setLayoutData(BorderLayout.CENTER);
-		
+
 		table = new Table(sashForm, SWT.BORDER | SWT.FULL_SELECTION);
 		table.setHeaderVisible(true);
 		table.setLinesVisible(true);
-		
+
 		TableColumn tblclmnColumn = new TableColumn(table, SWT.NONE);
 		tblclmnColumn.setWidth(100);
 		tblclmnColumn.setText("Column");
-		
+
 		TableColumn tblclmnRdfTerm = new TableColumn(table, SWT.NONE);
 		tblclmnRdfTerm.setWidth(200);
 		tblclmnRdfTerm.setText("Ontology Term");
-		
+
 		Tree tree = new Tree(sashForm, SWT.BORDER | SWT.FULL_SELECTION);
 		tree.setLinesVisible(true);
 		tree.setHeaderVisible(true);
-		
+
 		TreeColumn trclmnTerms = new TreeColumn(tree, SWT.NONE);
 		trclmnTerms.setWidth(200);
 		trclmnTerms.setText("Terms");
-		
+
 		TreeColumn trclmnUrl = new TreeColumn(tree, SWT.NONE);
 		trclmnUrl.setWidth(100);
 		trclmnUrl.setText("URL");
-		
+
 		TreeItem trtmSomeTree = new TreeItem(tree, SWT.NONE);
 		trtmSomeTree.setChecked(true);
 		trtmSomeTree.setText("Some tree");
 		trtmSomeTree.setExpanded(true);
-		
+
 		TreeItem trtmNewTreeitem_1 = new TreeItem(tree, SWT.NONE);
 		trtmNewTreeitem_1.setText("Bugger");
-		
+
 		TreeItem trtmNewTreeitem = new TreeItem(tree, SWT.NONE);
-		trtmNewTreeitem.setText(new String[] {"Alpha", "beta"});
+		trtmNewTreeitem.setText(new String[] { "Alpha", "beta" });
 		trtmNewTreeitem.setText("Another treee");
-		sashForm.setWeights(new int[] {310, 239});
+		sashForm.setWeights(new int[] { 310, 239 });
 
 	}
 }

anno-gui/src/main/java/org/genesys2/anno/gui/ColumnDefs.java

@@ -32,12 +32,12 @@ public class ColumnDefs extends AbstractModelObject {
 	public List<ColumnDef> getColumnDefs() {
 		return columnDefs;
 	}
-//
-//	public void addDataSource() {
-//		firePropertyChange("columnDefs", null, this);
-//	}
-//
-//	public void removeDataSource() {
-//		firePropertyChange("columnDefs", null, this);
-//	}
+	//
+	// public void addDataSource() {
+	// firePropertyChange("columnDefs", null, this);
+	// }
+	//
+	// public void removeDataSource() {
+	// firePropertyChange("columnDefs", null, this);
+	// }
 }

anno-gui/src/main/java/org/genesys2/anno/gui/DSW.java

@@ -26,7 +26,7 @@ public class DSW extends AbstractModelObject {
 	public IDataSourceSheet getDataSourceSheet() {
 		return dataSourceSheet;
 	}
-	
+
 	public CsvDataSourceSheet getCsvDataSourceSheet() {
 		return (CsvDataSourceSheet) (dataSourceSheet instanceof CsvDataSourceSheet ? dataSourceSheet : null);
 	}

anno-gui/src/main/java/org/genesys2/anno/gui/DataSourceFile.java

@@ -24,28 +24,28 @@ public class DataSourceFile extends AbstractModelObject implements IDataSource {
 	private File file;
 	private List<IDataSourceSheet> sheets = new ArrayList<IDataSourceSheet>();
 
-    @Override
+	@Override
 	public File getFile() {
 		return file;
 	}
 
-    @Override
+	@Override
 	public void setFile(File file) {
 		this.file = file;
 		firePropertyChange("fileName", null, file);
 	}
 
-    @Override
+	@Override
 	public String getFileName() {
-		return this.file==null ? null : this.file.getName();
+		return this.file == null ? null : this.file.getName();
 	}
 
-    @Override
+	@Override
 	public List<IDataSourceSheet> getSheets() {
 		return sheets;
 	}
 
-    @Override
+	@Override
 	public void setSheets(List<IDataSourceSheet> sheets) {
 		this.sheets = sheets;
 		firePropertyChange("sheets", null, sheets);

anno-gui/src/main/java/org/genesys2/anno/gui/DataSourceLoaderImpl.java

@@ -41,7 +41,7 @@ public class DataSourceLoaderImpl implements DataSourceLoader {
 
 	@Autowired
 	private JDBCRowReader jdbcRowReader;
-	
+
 	@Override
 	public void registerParser(DataSourceParser parser) {
 		_log.debug("Adding parser " + parser.getClass().getName());
@@ -116,17 +116,17 @@ public class DataSourceLoaderImpl implements DataSourceLoader {
 	@Override
 	public RowReader createRowReader(IDataSourceSheet sheet) throws IOException, UnsupportedDataFormatException {
 		// Iterate over parsers and see if something comes out
-		
+
 		if (sheet instanceof JdbcDataSourceSheet) {
-	        JdbcDataSourceSheet jdbcSheet = (JdbcDataSourceSheet) sheet;
+			JdbcDataSourceSheet jdbcSheet = (JdbcDataSourceSheet) sheet;
 			DatabaseSettings databaseSettings = jdbcSheet.getDatabaseSettings();
 			String url = databaseSettings.getUrl();
-	        String user = databaseSettings.getUser();
-	        String password = databaseSettings.getPassword();
+			String user = databaseSettings.getUser();
+			String password = databaseSettings.getPassword();
 
 			return jdbcRowReader.createRowReader(jdbcSheet.getQuery(), url, user, password);
 		}
-		
+
 		for (DataSourceParser parser : parsers) {
 			try {
 				if (parser.supports(sheet.getSourceFile())) {

anno-gui/src/main/java/org/genesys2/anno/gui/DataSourceParser.java

@@ -28,8 +28,7 @@ public interface DataSourceParser {
 
 	boolean supports(File sourceFile);
 
-	Collection<? extends DataSourceSheet> findSheets(File sourceFile)
-			throws UnsupportedDataFormatException;
+	Collection<? extends DataSourceSheet> findSheets(File sourceFile) throws UnsupportedDataFormatException;
 
 	List<Object[]> loadRows(IDataSourceSheet sheet, int maxRows, int startAt) throws UnsupportedDataFormatException, FileNotFoundException, IOException;
 

anno-gui/src/main/java/org/genesys2/anno/gui/DataSourceSheet.java

@@ -44,15 +44,17 @@ public class DataSourceSheet extends AbstractModelObject implements IDataSourceS
 		this.sourceFile = new File(sourceFile.getAbsolutePath());
 	}
 
+	@Override
 	public File getSourceFile() {
 		return sourceFile;
 	}
 
-    @Override
+	@Override
 	public String getSheetName() {
 		return sheetName;
 	}
 
+	@Override
 	public void setSheetName(String sheetName) {
 		this.sheetName = sheetName;
 		firePropertyChange("sheetName", null, sheetName);
@@ -76,30 +78,31 @@ public class DataSourceSheet extends AbstractModelObject implements IDataSourceS
 		firePropertyChange("columnTerms", null, columnTerms);
 	}
 
-    @Override
+	@Override
 	public void setHeadersIncluded(boolean headersIncluded) {
 		_log.debug("Set headers included :" + headersIncluded);
 		this.headersIncluded = headersIncluded;
 		firePropertyChange("headersIncluded", null, headersIncluded);
 	}
-    @Override
+
+	@Override
 	public boolean isHeadersIncluded() {
 		return headersIncluded;
 	}
 
-    @Override
+	@Override
 	public int getHeaderRowIndex() {
 		return headerRowIndex;
 	}
 
-    @Override
+	@Override
 	public void setHeaderRowIndex(int headerRowIndex) {
 		_log.debug("Set header row index:" + headerRowIndex);
 		this.headerRowIndex = headerRowIndex;
 		firePropertyChange("headerRowIndex", null, headerRowIndex);
 	}
 
-    @Override
+	@Override
 	public void updateData(List<Object[]> rows) {
 		int columnCount = 0;
 		for (Object[] row : rows) {
@@ -152,17 +155,17 @@ public class DataSourceSheet extends AbstractModelObject implements IDataSourceS
 			firePropertyChange("columns", null, columns);
 	}
 
-    @Override
+	@Override
 	public List<Object[]> getSampleData() {
 		return sampleData;
 	}
 
-    @Override
+	@Override
 	public List<Column> getColumns() {
 		return this.columns;
 	}
 
-    @Override